Total biological productivity and soil microbial biomass are important characteristics to describe sustainable agroecosystems. We investigated the impact of herbicide, alone or in combination with soil amendments, on crop and weed productivity and microbial biomass in a rice ( Oryza sativa)-barley ( Hordeum vulgare)-summer fallow rotation in a tropical rainfed agroecosystem. Total net productivity (TNP) of crops was greater with herbicide (Butachlor)+chemical fertilizer (NPK), herbicide+farmyard animal manure, and herbicide+green manure ( Sesbania aculeata) than with herbicide+crop residue ( Triticum aestivum straw), herbicide only, and the control without amendment. Weed TNP was highest in the control, lowest in herbicide only, and intermediate in combined herbicide and amendment treatments except herbicide+crop residue. The sum of crop TNP and weed TNP was highest in herbicide+green manure and lowest in herbicide only. Microbial biomass C and N were greater with herbicide and amendment treatments than with herbicide only. Microbial biomass showed distinct temporal variation. Yearly plant input to soil had strong correlation with microbial biomass in the control and herbicide only treatments. In these agroecosystems, combining organic soil amendments with herbicide application could help sustain soil fertility and maintain higher total biological productivity.